Getting the optics right
Fact #1: Copper is faster and cheaper than glass. Signals propagate faster through copper than glass, but that isn't the reason for going with copper over short distances.

The real win is cost: optical connectors rely on lasers and precision optical components that aren't cheap. They'll get there, but for most early users copper links will be fine.

Fact #2: Copper is widely used today in the storage world's high-end Fibre Channel for the same cost reasons. Most FC gear has a swappable transceiver module so you can choose to use copper or glass as needed.

Fact #3: The transceiver is where the choice between copper and fiber is made. It doesn't matter to the electronics on the other side of the transceiver. Therefore it doesn't affect your apps or the rest of the system architecture.

The tradeoffs
Glass fiber has some clear differences with copper, but they're only advantages if you need them.

EMI. Electro-Magnetic Interference is a growing problem with high-speed signalling. USB 3.0 is at the ragged edge of acceptable EMI today - and standards may get stricter. Glass is cleaner and much harder to tap as well.

The Storage Bits take
Given Light Peak's purported 10 Gb/sec speed, copper Light Peak will be lucky to support a 2 meter cable - plenty for notebook users - the same as copper eSATA. In a docking configuration, the dock could have optical transceivers for plugging into high-performance remote storage.

It will take time to get optical component production to the level that cuts prices. The same was true of optical Fibre Channel.

Having cheaper Light Peak components is the goal, and copper is the fastest way to achieve that. Longer term though, optical will enable faster and more flexible configurations.